1
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Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Brady RA, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. ACS CENTRAL SCIENCE 2024; 10:1262-1275. [PMID: 38947208 PMCID: PMC11212133 DOI: 10.1021/acscentsci.4c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to expand the chemical space available to biological therapeutics and materials, but existing technologies are still limiting. Addressing these limitations requires a deeper understanding of the mechanism of protein synthesis and how it is perturbed by nnAAs. Here we examine the impact of nnAAs on the formation and ribosome utilization of the central elongation substrate: the ternary complex of native, aminoacylated tRNA, thermally unstable elongation factor, and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer measurements, we reveal that both the (R)- and (S)-β2 isomers of phenylalanine (Phe) disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by 1 order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of translocation after mRNA decoding. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include the consideration of the efficiency and stability of ternary complex formation.
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Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wezley C. Griffin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuk-Cheung Chan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Maxwell I. Martin
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jose L. Alejo
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Ryan A. Brady
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - S. Kundhavai Natchiar
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Isaac J. Knudson
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Roger B. Altman
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Alanna Schepartz
- College
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Molecular
and Cell Biology, University of California,
Berkeley, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
- Innovation
Investigator, ARC Institute, Palo Alto, California 94304, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Scott C. Blanchard
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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2
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Nagasawa Y, Nakayama M, Kato Y, Ogawa Y, Aribam SD, Tsugami Y, Iwata T, Mikami O, Sugiyama A, Onishi M, Hayashi T, Eguchi M. A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives. Microbiol Spectr 2024; 12:e0355723. [PMID: 38385737 PMCID: PMC10986568 DOI: 10.1128/spectrum.03557-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after the removal of the uAA. The survival time after uAA removal could be controlled by the choice of the uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105 fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates. IMPORTANCE Live vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of uAAs to control gene expression and to conditionally kill host bacteria as a biological containment system. This report proposes a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system. The balance between safety and immunogenicity can be modulated by the selection of the genetic devices used. Moreover, the uAA-auxotrophy can prevent the vaccine from infecting other individuals or establishing the environment.
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Affiliation(s)
- Yuya Nagasawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Momoko Nakayama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusuke Kato
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Swarmistha Devi Aribam
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yusaku Tsugami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Osamu Mikami
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Aoi Sugiyama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Megumi Onishi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Tomohito Hayashi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Sapporo, Hokkaido, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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4
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Cruz-Navarrete FA, Griffin WC, Chan YC, Martin MI, Alejo JL, Natchiar SK, Knudson IJ, Altman RB, Schepartz A, Miller SJ, Blanchard SC. β-amino acids reduce ternary complex stability and alter the translation elongation mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581891. [PMID: 38464221 PMCID: PMC10925103 DOI: 10.1101/2024.02.24.581891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to vastly expand the chemical space available to biological therapeutics and materials. Existing technologies limit the identity and number of nnAAs than can be incorporated into a given protein. Addressing these bottlenecks requires deeper understanding of the mechanism of messenger RNA (mRNA) templated protein synthesis and how this mechanism is perturbed by nnAAs. Here we examine the impact of both monomer backbone and side chain on formation and ribosome-utilization of the central protein synthesis substate: the ternary complex of native, aminoacylated transfer RNA (aa-tRNA), thermally unstable elongation factor (EF-Tu), and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer (FRET) measurements, we reveal the dramatic effect of monomer backbone on ternary complex formation and protein synthesis. Both the (R) and (S)-β2 isomers of Phe disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β3-Phe reduce ternary complex stability by approximately one order of magnitude. Consistent with these findings, (R)- and (S)-β2-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β3-Phe stereoisomers were utilized inefficiently. The reduced affinities of both species for EF-Tu ostensibly bypassed the proofreading stage of mRNA decoding. (R)-β3-Phe but not (S)-β3-Phe also exhibited order of magnitude defects in the rate of substrate translocation after mRNA decoding, in line with defects in peptide bond formation that have been observed for D-α-Phe. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include consideration of the efficiency and stability of ternary complex formation.
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Affiliation(s)
- F. Aaron Cruz-Navarrete
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Wezley C. Griffin
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yuk-Cheung Chan
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Maxwell I. Martin
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jose L. Alejo
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - S. Kundhavai Natchiar
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Isaac J. Knudson
- College of Chemistry, University of California, Berkeley, California, USA
| | - Roger B. Altman
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Alanna Schepartz
- College of Chemistry, University of California, Berkeley, California, USA
- Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Innovation Investigator, ARC Institute, Palo Alto, CA 94304, USA
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Scott C. Blanchard
- Department of Structural Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Chemical Biology & Therapeutics, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
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5
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Liu F, He L, Dong S, Xuan J, Cui Q, Feng Y. Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges. Molecules 2023; 28:5850. [PMID: 37570818 PMCID: PMC10421094 DOI: 10.3390/molecules28155850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.
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Affiliation(s)
- Fenghua Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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7
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Lee K, Willi JA, Cho N, Kim I, Jewett MC, Lee J. Cell-free Biosynthesis of Peptidomimetics. BIOTECHNOL BIOPROC E 2023; 28:1-17. [PMID: 36778039 PMCID: PMC9896473 DOI: 10.1007/s12257-022-0268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/16/2022] [Accepted: 11/13/2022] [Indexed: 02/05/2023]
Abstract
A wide variety of peptidomimetics (peptide analogs) possessing innovative biological functions have been brought forth as therapeutic candidates through cell-free protein synthesis (CFPS) systems. A key feature of these peptidomimetic drugs is the use of non-canonical amino acid building blocks with diverse biochemical properties that expand functional diversity. Here, we summarize recent technologies leveraging CFPS platforms to expand the reach of peptidomimetics drugs. We also offer perspectives on engineering the translational machinery that may open new opportunities for expanding genetically encoded chemistry to transform drug discovery practice beyond traditional boundaries.
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Affiliation(s)
- Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Jessica A. Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Inseon Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Joongoo Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673 Korea
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8
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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9
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Ganesh RB, Maerkl SJ. Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications. Front Bioeng Biotechnol 2022; 10:918659. [PMID: 35845409 PMCID: PMC9283866 DOI: 10.3389/fbioe.2022.918659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of transcription and translation steps to decode genetic information. Aminoacyl tRNA synthetases (AARSs) and tRNAs are key components involved in translation and thus protein synthesis. This review provides information on AARSs and tRNA biochemistry, their role in the translation process, summarizes progress in cell-free engineering of tRNAs and AARSs, and discusses prospects and challenges lying ahead in cell-free engineering.
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10
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Fu X, Huang Y, Shen Y. Improving the Efficiency and Orthogonality of Genetic Code Expansion. BIODESIGN RESEARCH 2022; 2022:9896125. [PMID: 37850140 PMCID: PMC10521639 DOI: 10.34133/2022/9896125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/20/2022] [Indexed: 10/19/2023] Open
Abstract
The site-specific incorporation of the noncanonical amino acid (ncAA) into proteins via genetic code expansion (GCE) has enabled the development of new and powerful ways to learn, regulate, and evolve biological functions in vivo. However, cellular biosynthesis of ncAA-containing proteins with high efficiency and fidelity is a formidable challenge. In this review, we summarize up-to-date progress towards improving the efficiency and orthogonality of GCE and enhancing intracellular compatibility of introduced translation machinery in the living cells by creation and optimization of orthogonal translation components, constructing genomically recoded organism (GRO), utilization of unnatural base pairs (UBP) and quadruplet codons (four-base codons), and spatial separation of orthogonal translation.
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Affiliation(s)
- Xian Fu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120China
| | - Yijian Huang
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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11
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Hans S, Kumar N, Gohil N, Khambhati K, Bhattacharjee G, Deb SS, Maurya R, Kumar V, Reshamwala SMS, Singh V. Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms. Microb Cell Fact 2022; 21:100. [PMID: 35643549 PMCID: PMC9148472 DOI: 10.1186/s12934-022-01828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022] Open
Abstract
The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.
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12
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Perez JG, Carlson ED, Weisser O, Kofman C, Seki K, Des Soye BJ, Karim AS, Jewett MC. Improving genomically recoded Escherichia coli to produce proteins containing non-canonical amino acids. Biotechnol J 2022; 17:e2100330. [PMID: 34894206 DOI: 10.1002/biot.202100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
Abstract
A genomically recoded Escherichia coli strain that lacks all amber codons and release factor 1 (C321.∆A) enables efficient genetic encoding of chemically diverse non-canonical amino acids (ncAAs) into proteins. While C321.∆A has opened new opportunities in chemical and synthetic biology, this strain has not been optimized for protein production, limiting its utility in widespread industrial and academic applications. To address this limitation, the construction of a series of genomically recoded organisms that are optimized for cellular protein production is described. It is demonstrated that the functional deactivation of nucleases (e.g., rne, endA) and proteases (e.g., lon) increases production of wild-type superfolder green fluorescent protein (sfGFP) and sfGFP containing two ncAAs up to ≈5-fold. Additionally, a genomic IPTG-inducible T7 RNA polymerase (T7RNAP) cassette into these strains is introduced. Using an optimized platform, the ability to introduce two identical N6 -(propargyloxycarbonyl)-L -Lysine residues site specifically into sfGFP with a 17-fold improvement in production relative to the parent strain is demonstrated. The authors envision that their library of organisms will provide the community with multiple options for increased expression of proteins with new and diverse chemistries.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Oliver Weisser
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Benjamin J Des Soye
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois, USA
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13
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14
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Thyer R, d'Oelsnitz S, Blevins MS, Klein DR, Brodbelt JS, Ellington AD. Directed Evolution of an Improved Aminoacyl‐tRNA Synthetase for Incorporation of L‐3,4‐Dihydroxyphenylalanine (L‐DOPA). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ross Thyer
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
- Department of Chemical and Biomolecular Engineering Rice University Houston TX USA
| | - Simon d'Oelsnitz
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
| | - Molly S. Blevins
- Department of Chemistry The University of Texas at Austin Austin TX USA
| | - Dustin R. Klein
- Department of Chemistry The University of Texas at Austin Austin TX USA
| | | | - Andrew D. Ellington
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
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15
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Thyer R, d'Oelsnitz S, Blevins MS, Klein DR, Brodbelt JS, Ellington AD. Directed Evolution of an Improved Aminoacyl-tRNA Synthetase for Incorporation of L-3,4-Dihydroxyphenylalanine (L-DOPA). Angew Chem Int Ed Engl 2021; 60:14811-14816. [PMID: 33871147 DOI: 10.1002/anie.202100579] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/24/2021] [Indexed: 11/07/2022]
Abstract
The catechol group of 3,4-dihydroxyphenylalanine (L-DOPA) derived from L-tyrosine oxidation is a key post-translational modification (PTM) in many protein biomaterials and has potential as a bioorthogonal handle for precision protein conjugation applications such as antibody-drug conjugates. Despite this potential, indiscriminate enzymatic modification of exposed tyrosine residues or complete replacement of tyrosine using auxotrophic hosts remains the preferred method of introducing the catechol moiety into proteins, which precludes many protein engineering applications. We have developed new orthogonal translation machinery to site-specifically incorporate L-DOPA into recombinant proteins and a new fluorescent biosensor to selectively monitor L-DOPA incorporation in vivo. We show simultaneous biosynthesis and incorporation of L-DOPA and apply this translation machinery to engineer a novel metalloprotein containing a DOPA-Fe chromophore.
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Affiliation(s)
- Ross Thyer
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Simon d'Oelsnitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Molly S Blevins
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Dustin R Klein
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | | | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
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16
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Incorporation of backbone modifications in mRNA-displayable peptides. Methods Enzymol 2021; 656:521-544. [PMID: 34325797 DOI: 10.1016/bs.mie.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we comprehensively summarize the most recent efforts in our research team, aiming at installing N-methyl and azole backbones into peptides expressed in translation. The genetic code reprogramming using the Flexible In-vitro Translation system (FIT system) has proven to be the most reliable and versatile approach for ribosomally installing various exotic amino acids. However, it had been yet difficult in translating diverse kinds of multiple and consecutive sequences of N-methyl amino acids (MeAAs). We have recently reported that a semi-rational fine tuning of MeAA-tRNA affinities for EF-Tu by altering tRNA T-stem sequence achieves efficient delivery of MeAA-tRNAs to the ribosome. Indeed, this approach has made it possible to express N-methyl-peptides containing multiple MeAAs with a remarkably high fidelity. Another interesting backbone modification in peptides is azole moieties often found in natural products, but they are explicitly installed by post-translational modifying enzymes. We have recently devised a method to bypass such enzymatic processes where a bromovinyl group-containing amino acid is incorporated into the peptide by genetic code reprogramming and then chemically converted to an azole group via an intramolecular heterocyclization reaction. These methods will grant more drug-like properties to peptides than ordinary peptides in terms of protease resistance and cell membrane permeability. Particularly when they can be integrated with in vitro mRNA display, such as the RaPID system, the discovery of de novo bioactive peptides can be realized.
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17
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Kofman C, Lee J, Jewett MC. Engineering molecular translation systems. Cell Syst 2021; 12:593-607. [PMID: 34139167 DOI: 10.1016/j.cels.2021.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/19/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Molecular translation systems provide a genetically encoded framework for protein synthesis, which is essential for all life. Engineering these systems to incorporate non-canonical amino acids (ncAAs) into peptides and proteins has opened many exciting opportunities in chemical and synthetic biology. Here, we review recent advances that are transforming our ability to engineer molecular translation systems. In cell-based systems, new processes to synthesize recoded genomes, tether ribosomal subunits, and engineer orthogonality with high-throughput workflows have emerged. In cell-free systems, adoption of flexizyme technology and cell-free ribosome synthesis and evolution platforms are expanding the limits of chemistry at the ribosome's RNA-based active site. Looking forward, innovations will deepen understanding of molecular translation and provide a path to polymers with previously unimaginable structures and functions.
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Affiliation(s)
- Camila Kofman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Interdisplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA; Simpson Querrey Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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18
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Iwane Y, Kimura H, Katoh T, Suga H. Uniform affinity-tuning of N-methyl-aminoacyl-tRNAs to EF-Tu enhances their multiple incorporation. Nucleic Acids Res 2021; 49:10807-10817. [PMID: 33997906 PMCID: PMC8565323 DOI: 10.1093/nar/gkab288] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023] Open
Abstract
In ribosomal translation, the accommodation of aminoacyl-tRNAs into the ribosome is mediated by elongation factor thermo unstable (EF-Tu). The structures of proteinogenic aminoacyl-tRNAs (pAA-tRNAs) are fine-tuned to have uniform binding affinities to EF-Tu in order that all proteinogenic amino acids can be incorporated into the nascent peptide chain with similar efficiencies. Although genetic code reprogramming has enabled the incorporation of non-proteinogenic amino acids (npAAs) into the nascent peptide chain, the incorporation of some npAAs, such as N-methyl-amino acids (MeAAs), is less efficient, especially when MeAAs frequently and/or consecutively appear in a peptide sequence. Such poor incorporation efficiencies can be attributed to inadequate affinities of MeAA-tRNAs to EF-Tu. Taking advantage of flexizymes, here we have experimentally verified that the affinities of MeAA-tRNAs to EF-Tu are indeed weaker than those of pAA-tRNAs. Since the T-stem of tRNA plays a major role in interacting with EF-Tu, we have engineered the T-stem sequence to tune the affinity of MeAA-tRNAs to EF-Tu. The uniform affinity-tuning of the individual pairs has successfully enhanced the incorporation of MeAAs, achieving the incorporation of nine distinct MeAAs into both linear and thioether-macrocyclic peptide scaffolds.
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Affiliation(s)
- Yoshihiko Iwane
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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19
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Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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20
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Williams TL, Iskandar DJ, Nödling AR, Tan Y, Luk LYP, Tsai YH. Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency. Amino Acids 2020; 53:89-96. [PMID: 33331978 PMCID: PMC7822784 DOI: 10.1007/s00726-020-02927-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 10/31/2022]
Abstract
Genetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.
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Affiliation(s)
| | | | | | - Yurong Tan
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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21
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Abstract
Within the broad field of synthetic biology, genetic code expansion (GCE) techniques enable creation of proteins with an expanded set of amino acids. This may be invaluable for applications in therapeutics, bioremediation, and biocatalysis. Central to GCE are aminoacyl-tRNA synthetases (aaRSs) as they link a non-canonical amino acid (ncAA) to their cognate tRNA, allowing ncAA incorporation into proteins on the ribosome. The ncAA-acylating aaRSs and their tRNAs should not cross-react with 20 natural aaRSs and tRNAs in the host, i.e., they need to function as an orthogonal translating system. All current orthogonal aaRS•tRNA pairs have been engineered from naturally occurring molecules to change the aaRS's amino acid specificity or assign the tRNA to a liberated codon of choice. Here we discuss the importance of orthogonality in GCE, laboratory techniques employed to create designer aaRSs and tRNAs, and provide an overview of orthogonal aaRS•tRNA pairs for GCE purposes.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
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22
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Wu Y, Wang Z, Qiao X, Li J, Shu X, Qi H. Emerging Methods for Efficient and Extensive Incorporation of Non-canonical Amino Acids Using Cell-Free Systems. Front Bioeng Biotechnol 2020; 8:863. [PMID: 32793583 PMCID: PMC7387428 DOI: 10.3389/fbioe.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cell-free protein synthesis (CFPS) has emerged as a novel protein expression platform. Especially the incorporation of non-canonical amino acids (ncAAs) has led to the development of numerous flexible methods for efficient and extensive expression of artificial proteins. Approaches were developed to eliminate the endogenous competition for ncAAs and engineer translation factors, which significantly enhanced the incorporation efficiency. Furthermore, in vitro aminoacylation methods can be conveniently combined with cell-free systems, extensively expanding the available ncAAs with novel and unique moieties. In this review, we summarize the recent progresses on the efficient and extensive incorporation of ncAAs by different strategies based on the elimination of competition by endogenous factors, translation factors engineering and extensive incorporation of novel ncAAs coupled with in vitro aminoacylation methods in CFPS. We also aim to offer new ideas to researchers working on ncAA incorporation techniques in CFPS and applications in various emerging fields.
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Affiliation(s)
- Yang Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xiangrong Shu
- Department of Pharmacy, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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23
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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24
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Wang T, Liang C, Xu H, An Y, Xiao S, Zheng M, Liu L, Nie L. Incorporation of nonstandard amino acids into proteins: principles and applications. World J Microbiol Biotechnol 2020; 36:60. [PMID: 32266578 DOI: 10.1007/s11274-020-02837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 01/01/2023]
Abstract
The cellular ribosome shows a naturally evolved strong preference for the synthesis of proteins with standard amino acids. An in-depth understanding of the translation process enables scientists to go beyond this natural limitation and engineer translating systems capable of synthesizing proteins with artificially designed and synthesized non-standard amino acids (nsAA) featuring more bulky sidechains. The sidechains can be functional groups, with chosen biophysical or chemical activities, that enable the direct application of these proteins. Alternatively, the sidechains can be designed to contain highly reactive groups: enabling the ready formation of conjugates via a covalent bond between the sidechain and other chemicals or biomolecules. This co-translational incorporation of nsAAs into proteins allows for a vast number of possible applications. In this paper, we first systematically summarized the advances in the engineering of the translation system. Subsequently, we reviewed the extensive applications of these nsAA-containing proteins (after chemical modification) by discussing representative reports on how they can be utilized for different purposes. Finally, we discussed the direction of further studies which could be undertaken to improve the current technology utilized in incorporating nsAAs in order to use them to their full potential and improve accessibility across disciplines.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Hongjv Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yafei An
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Sha Xiao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Mengyuan Zheng
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lu Liu
- College of International Education, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lei Nie
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China.
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25
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26
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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27
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Potts KA, Stieglitz JT, Lei M, Van Deventer JA. Reporter system architecture affects measurements of noncanonical amino acid incorporation efficiency and fidelity. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:573-588. [PMID: 33791108 PMCID: PMC8009230 DOI: 10.1039/c9me00107g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) within proteins supports a growing number of applications ranging from fundamental biological studies to enhancing the properties of biological therapeutics. Currently, our quantitative understanding of ncAA incorporation systems is confounded by the diverse set of characterization and analysis approaches used to quantify ncAA incorporation events. While several effective reporter systems support such measurements, it is not clear how quantitative results from different reporters relate to one another, or which details influence measurements most strongly. Here, we evaluate the quantitative performance of single-fluorescent protein reporters, dual-fluorescent protein reporters, and cell surface-displayed protein reporters of ncAA insertion in response to the TAG (amber) codon in yeast. While different reporters support varying levels of apparent readthrough efficiencies, flow cytometry-based evaluations with dual reporters yielded measurements exhibiting consistent quantitative trends and precision across all evaluated conditions. Further investigations of dual-fluorescent protein reporter architecture revealed that quantitative outputs are influenced by stop codon location and N- and C-terminal fluorescent protein identity. Both dual-fluorescent protein reporters and a "drop-in" version of yeast display support quantification of ncAA incorporation in several single-gene knockout strains, revealing strains that enhance ncAA incorporation efficiency without compromising fidelity. Our studies reveal critical details regarding reporter system performance in yeast and how to effectively deploy such reporters. These findings have substantial implications for how to engineer ncAA incorporation systems-and protein translation apparatuses-to better accommodate alternative genetic codes for expanding the chemical diversity of biosynthesized proteins.
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Affiliation(s)
- K A Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J T Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - M Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - J A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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28
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Hunt JP, Zhao EL, Soltani M, Frei M, Nelson JAD, Bundy BC. Streamlining the preparation of "endotoxin-free" ClearColi cell extract with autoinduction media for cell-free protein synthesis of the therapeutic protein crisantaspase. Synth Syst Biotechnol 2019; 4:220-224. [PMID: 31890926 PMCID: PMC6926305 DOI: 10.1016/j.synbio.2019.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
An "endotoxin-free" E. coli-based cell-free protein synthesis system has been reported to produce therapeutic proteins rapidly and on-demand. However, preparation of the most complex CFPS reagent - the cell extract - remains time-consuming and labor-intensive because of the relatively slow growth kinetics of the endotoxin-free ClearColiTMBL21(DE3) strain. Here we report a streamlined procedure for preparing E. coli cell extract from ClearColi™ using auto-induction media. In this work, the term auto-induction describes cell culture media which eliminates the need for manual induction of protein expression. Culturing Clearcoli™ cells in autoinduction media significantly reduces the hands-on time required during extract preparation, and the resulting "endotoxin-free" cell extract maintained the same cell-free protein synthesis capability as extract produced with traditional induction as demonstrated by the high-yield expression of crisantaspase, an FDA approved leukemia therapeutic. It is anticipated that this work will lower the barrier for researchers to enter the field and use this technology as the method to produce endotoxin-free E. coli-based extract for CFPS.
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Affiliation(s)
| | | | | | | | | | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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29
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Des Soye BJ, Gerbasi VR, Thomas PM, Kelleher NL, Jewett MC. A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli. Cell Chem Biol 2019; 26:1743-1754.e9. [PMID: 31706984 DOI: 10.1016/j.chembiol.2019.10.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 (RF1) competition has limited this technology. To address this limitation, we develop a high-yield, one-pot cell-free platform for synthesizing proteins bearing ncAAs based on genomically recoded Escherichia coli lacking RF1. A key feature of this platform is the independence on the addition of purified T7 DNA-directed RNA polymerase (T7RNAP) to catalyze transcription. Extracts derived from our final strain demonstrate high productivity, synthesizing 2.67 ± 0.06 g/L superfolder GFP in batch mode without supplementation of purified T7RNAP. Using an optimized one-pot platform, we demonstrate multi-site incorporation of the ncAA p-acetyl-L-phenylalanine into an elastin-like polypeptide with high accuracy of incorporation and yield. Our work has implications for chemical and synthetic biology.
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Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Vincent R Gerbasi
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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30
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Israeli B, Vaserman L, Amiram M. Multi‐Site Incorporation of Nonstandard Amino Acids into Protein‐Based Biomaterials. Isr J Chem 2019. [DOI: 10.1002/ijch.201900043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bar Israeli
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering Ben-Gurion University of the Negev Beer-Sheva Israel
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31
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Engineered ribosomes with tethered subunits for expanding biological function. Nat Commun 2019; 10:3920. [PMID: 31477696 PMCID: PMC6718428 DOI: 10.1038/s41467-019-11427-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/10/2019] [Indexed: 01/01/2023] Open
Abstract
Ribo-T is a ribosome with covalently tethered subunits where core 16S and 23S ribosomal RNAs form a single chimeric molecule. Ribo-T makes possible a functionally orthogonal ribosome-mRNA system in cells. Unfortunately, use of Ribo-T has been limited because of low activity of its original version. Here, to overcome this limitation, we use an evolutionary approach to select new tether designs that are capable of supporting faster cell growth and increased protein expression. Further, we evolve new orthogonal Ribo-T/mRNA pairs that function in parallel with, but independent of, natural ribosomes and mRNAs, increasing the efficiency of orthogonal protein expression. The Ribo-T with optimized designs is able to synthesize a diverse set of proteins, and can also incorporate multiple non-canonical amino acids into synthesized polypeptides. The enhanced Ribo-T designs should be useful for exploring poorly understood functions of the ribosome and engineering ribosomes with altered catalytic properties.
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32
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Smolskaya S, Andreev YA. Site-Specific Incorporation of Unnatural Amino Acids into Escherichia coli Recombinant Protein: Methodology Development and Recent Achievement. Biomolecules 2019; 9:biom9070255. [PMID: 31261745 PMCID: PMC6681230 DOI: 10.3390/biom9070255] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
More than two decades ago a general method to genetically encode noncanonical or unnatural amino acids (NAAs) with diverse physical, chemical, or biological properties in bacteria, yeast, animals and mammalian cells was developed. More than 200 NAAs have been incorporated into recombinant proteins by means of non-endogenous aminoacyl-tRNA synthetase (aa-RS)/tRNA pair, an orthogonal pair, that directs site-specific incorporation of NAA encoded by a unique codon. The most established method to genetically encode NAAs in Escherichia coli is based on the usage of the desired mutant of Methanocaldococcus janaschii tyrosyl-tRNA synthetase (MjTyrRS) and cognate suppressor tRNA. The amber codon, the least-used stop codon in E. coli, assigns NAA. Until very recently the genetic code expansion technology suffered from a low yield of targeted proteins due to both incompatibilities of orthogonal pair with host cell translational machinery and the competition of suppressor tRNA with release factor (RF) for binding to nonsense codons. Here we describe the latest progress made to enhance nonsense suppression in E. coli with the emphasis on the improved expression vectors encoding for an orthogonal aa-RA/tRNA pair, enhancement of aa-RS and suppressor tRNA efficiency, the evolution of orthogonal EF-Tu and attempts to reduce the effect of RF1.
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Affiliation(s)
- Sviatlana Smolskaya
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
| | - Yaroslav A Andreev
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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33
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Baumann T, Hauf M, Richter F, Albers S, Möglich A, Ignatova Z, Budisa N. Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine. Int J Mol Sci 2019; 20:ijms20092343. [PMID: 31083552 PMCID: PMC6539999 DOI: 10.3390/ijms20092343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/20/2023] Open
Abstract
Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants. For aaRS enzyme redesign, photocaged ortho-nitrobenzyl tyrosine (ONBY) was chosen as substrate due to commercial availability and its diverse applications. Diversifying 17 first- and second-shell sites and performing conventional aaRS positive and negative selection resulted in a high-activity aaRS. This MjTyrRS variant carries ten mutations and outperforms previously reported ONBY-specific aaRS variants isolated from traditional libraries. In response to a single in-frame amber stop codon, it mediates the in vivo incorporation of ONBY with an efficiency matching that of the wild type MjTyrRS enzyme acylating cognate tyrosine. These results exemplify an improved general strategy for aaRS library design and engineering.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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34
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Jin X, Park OJ, Hong SH. Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. Appl Microbiol Biotechnol 2019; 103:2947-2958. [PMID: 30790000 PMCID: PMC6449208 DOI: 10.1007/s00253-019-09690-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022]
Abstract
The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
- Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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35
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DeLey Cox VE, Cole MF, Gaucher EA. Incorporation of Modified Amino Acids by Engineered Elongation Factors with Expanded Substrate Capabilities. ACS Synth Biol 2019; 8:287-296. [PMID: 30609889 PMCID: PMC6379855 DOI: 10.1021/acssynbio.8b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Noncanonical
amino acid (ncAA) incorporation has led to significant
advances in protein science and engineering. Traditionally, in vivo incorporation of ncAAs is achieved via amber codon suppression using an engineered orthogonal aminoacyl-tRNA
synthetase:tRNA pair. However, as more complex protein products are
targeted, researchers are identifying additional barriers limiting
the scope of currently available ncAA systems. One barrier is elongation
factor Tu (EF-Tu), a protein responsible for proofreading aa-tRNAs,
which substantially restricts ncAA scope by limiting ncaa-tRNA delivery
to the ribosome. Researchers have responded by engineering ncAA-compatible
EF-Tus for key ncAAs. However, this approach fails to address the
extent to which EF-Tu inhibits efficient ncAA incorporation. Here,
we demonstrate an alternative strategy leveraging computational analysis
to broaden EF-Tu’s substrate specificity. Evolutionary analysis
of EF-Tu and a naturally evolved specialized elongation factor, SelB,
provide the opportunity to engineer EF-Tu by targeting amino acid
residues that are associated with functional divergence between the
two ancient paralogues. Employing amber codon suppression, in combination
with mass spectrometry, we identified two EF-Tu variants with non-native
substrate compatibility. Additionally, we present data showing these
EF-Tu variants contribute to host organismal fitness, working cooperatively
with components of native and engineered translation machinery. These
results demonstrate the viability of our computational method and
lend support to corresponding assumptions about molecular evolution.
This work promotes enhanced polyspecific EF-Tu behavior as a viable
strategy to expand ncAA scope and complements ongoing research emphasizing
the importance of a comprehensive approach to further expand the genetic
code.
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Affiliation(s)
- Vanessa E. DeLey Cox
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Megan F. Cole
- Department of Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Eric A. Gaucher
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
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36
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Efficient Incorporation of Unnatural Amino Acids into Proteins with a Robust Cell-Free System. Methods Protoc 2019; 2:mps2010016. [PMID: 31164598 PMCID: PMC6481062 DOI: 10.3390/mps2010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/25/2023] Open
Abstract
Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatural proteins by highly effective site-specific incorporation of unnatural amino acids (UNAAs), without the limitations of cell membrane permeability and the toxicity of unnatural components. Here, we describe a quick and simple method to synthesize unnatural proteins in CFPS system based on Escherichia coli crude extract, with unnatural orthogonal aminoacyl-tRNA synthetase and suppressor tRNA evolved from Methanocaldococcus jannaschii. The superfolder green fluorescent protein (sfGFP) and p-propargyloxyphenylalanine (pPaF) were used as the model protein and UNAA. The synthesis of unnatural sfGFPs was characterized by microplate spectrophotometer, affinity chromatography, and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). This protocol provides a detailed procedure guiding how to use the powerful CFPS system to synthesize unnatural proteins on demand.
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37
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Versatility of Synthetic tRNAs in Genetic Code Expansion. Genes (Basel) 2018; 9:genes9110537. [PMID: 30405060 PMCID: PMC6267555 DOI: 10.3390/genes9110537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022] Open
Abstract
Transfer RNA (tRNA) is a dynamic molecule used by all forms of life as a key component of the translation apparatus. Each tRNA is highly processed, structured, and modified, to accurately deliver amino acids to the ribosome for protein synthesis. The tRNA molecule is a critical component in synthetic biology methods for the synthesis of proteins designed to contain non-canonical amino acids (ncAAs). The multiple interactions and maturation requirements of a tRNA pose engineering challenges, but also offer tunable features. Major advances in the field of genetic code expansion have repeatedly demonstrated the central importance of suppressor tRNAs for efficient incorporation of ncAAs. Here we review the current status of two fundamentally different translation systems (TSs), selenocysteine (Sec)- and pyrrolysine (Pyl)-TSs. Idiosyncratic requirements of each of these TSs mandate how their tRNAs are adapted and dictate the techniques used to select or identify the best synthetic variants.
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38
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Chemla Y, Ozer E, Algov I, Alfonta L. Context effects of genetic code expansion by stop codon suppression. Curr Opin Chem Biol 2018; 46:146-155. [DOI: 10.1016/j.cbpa.2018.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/01/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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39
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Stieglitz JT, Kehoe HP, Lei M, Van Deventer JA. A Robust and Quantitative Reporter System To Evaluate Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2018; 7:2256-2269. [PMID: 30139255 PMCID: PMC6214617 DOI: 10.1021/acssynbio.8b00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering protein translation machinery to incorporate noncanonical amino acids (ncAAs) into proteins has advanced applications ranging from proteomics to single-molecule studies. As applications of ncAAs emerge, efficient ncAA incorporation is crucial to exploiting unique chemistries. We have established a quantitative reporter platform to evaluate ncAA incorporation in response to the TAG (amber) codon in yeast. This yeast display-based reporter utilizes an antibody fragment containing an amber codon at which a ncAA is incorporated when the appropriate orthogonal translation system (OTS) is present. Epitope tags at both termini allow for flow cytometry-based end point readouts of OTS efficiency and fidelity. Using this reporter, we evaluated several factors that influence amber suppression, including the amber codon position and different aminoacyl-tRNA synthetase/tRNA (aaRS/tRNA) pairs. Interestingly, previously described aaRSs that evolved from different parent enzymes to incorporate O-methyl-l-tyrosine exhibit vastly different behavior. Escherichia coli leucyl-tRNA synthetase variants demonstrated efficient incorporation of a range of ncAAs, and we discovered unreported activities of several variants. Compared to a plate reader-based reporter, our assay yields more precise bulk-level measurements while also supporting single-cell readouts compatible with cell sorting. This platform is expected to allow quantitative elucidation of principles dictating efficient stop codon suppression and evolution of next-generation stop codon suppression systems to further enhance genetic code manipulation in eukaryotes. These efforts will improve our understanding of how the genetic code can be further evolved while expanding the range of chemical diversity available in proteins for applications ranging from fundamental epigenetics studies to engineering new classes of therapeutics.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - Ming Lei
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, United States
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40
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Kato Y. Tight Translational Control Using Site-Specific Unnatural Amino Acid Incorporation with Positive Feedback Gene Circuits. ACS Synth Biol 2018; 7:1956-1963. [PMID: 29979867 DOI: 10.1021/acssynbio.8b00204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tight regulatory system for gene expression, which is ideally controlled by unnatural and bio-orthogonal substances, is a keystone for successful construction of synthetic gene circuits. Here, we present a widely applicable approach to construct tight protein translational switches using site-specific unnatural amino acid (Uaa) incorporation systems. As a key mechanism to obtain excellent tightness, we installed gene circuits for positive feedback derepression. This mechanism dramatically suppressed leakage translation in the absence of the Uaa. In a translational switch with the feedback circuit in Escherichia coli, a 1.4 × 103 ON/OFF ratio was achieved which was 3 × 102-fold greater than that of the parent system and was comparable to that of the well-known tight expression system using the araBAD promoter and the araC regulator. This method offers an avenue for generation of novel tight genetic switches from over a hundred site-specific unnatural amino acid incorporation systems which have already been established. These tight translational switches will facilitate the development of fine gene control systems in synthetic biology, especially for Uaa-auxotrophy-based biological containments and live attenuated vaccines.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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41
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Uhlenbeck OC, Schrader JM. Evolutionary tuning impacts the design of bacterial tRNAs for the incorporation of unnatural amino acids by ribosomes. Curr Opin Chem Biol 2018; 46:138-145. [PMID: 30059836 DOI: 10.1016/j.cbpa.2018.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/27/2018] [Accepted: 07/13/2018] [Indexed: 01/23/2023]
Abstract
In order to function on the ribosome with uniform rate and adequate accuracy, each bacterial tRNA has evolved to have a characteristic sequence and set of modifications that compensate for the differing physical properties of its esterified amino acid and its codon-anticodon interaction. The sequence of the T-stem of each tRNA compensates for the differential effect of the esterified amino acid on the binding and release of EF-Tu during decoding. The sequence and modifications in the anticodon loop and core of tRNA impact the codon-anticodon strength and the ability of the tRNA to bend during codon recognition. These discoveries impact the design of tRNAs for the efficient and accurate incorporation of unnatural amino acids into proteins using bacterial translation systems.
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Affiliation(s)
- Olke C Uhlenbeck
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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42
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Venkat S, Sturges J, Stahman A, Gregory C, Gan Q, Fan C. Genetically Incorporating Two Distinct Post-translational Modifications into One Protein Simultaneously. ACS Synth Biol 2018; 7:689-695. [PMID: 29301074 DOI: 10.1021/acssynbio.7b00408] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) play important roles in regulating a variety of biological processes. To facilitate PTM studies, the genetic code expansion strategy has been utilized to cotranslationally incorporate individual PTMs such as acetylation and phosphorylation into proteins at specific sites. However, recent studies have demonstrated that PTMs actually work together to regulate protein functions and structures. Thus, simultaneous incorporation of multiple distinct PTMs into one protein is highly desirable. In this study, we utilized the genetic incorporation systems of phosphoserine and acetyllysine to install both phosphorylation and acetylation into target proteins simultaneously in Escherichia coli. And we used this system to study the effect of coexisting acetylation and phosphorylation on malate dehydrogenase, demonstrating a practical application of this system in biochemical studies. Furthermore, we tested the mutual orthogonality of three widely used genetic incorporation systems, indicating the possibility of incorporating three distinct PTMs into one protein simultaneously.
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Affiliation(s)
- Sumana Venkat
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Jourdan Sturges
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Alleigh Stahman
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Caroline Gregory
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Qinglei Gan
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department
of Chemistry and Biochemistry, ‡Cell and Molecular Biology Program, and §Department of
Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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43
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Costa SA, Simon JR, Amiram M, Tang L, Zauscher S, Brustad EM, Isaacs FJ, Chilkoti A. Photo-Crosslinkable Unnatural Amino Acids Enable Facile Synthesis of Thermoresponsive Nano- to Microgels of Intrinsically Disordered Polypeptides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:10.1002/adma.201704878. [PMID: 29226470 PMCID: PMC5942558 DOI: 10.1002/adma.201704878] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/01/2017] [Indexed: 05/20/2023]
Abstract
Hydrogel particles are versatile materials that provide exquisite, tunable control over the sequestration and delivery of materials in pharmaceutics, tissue engineering, and photonics. The favorable properties of hydrogel particles depend largely on their size, and particles ranging from nanometers to micrometers are used in different applications. Previous studies have only successfully fabricated these particles in one specific size regime and required a variety of materials and fabrication methods. A simple yet powerful system is developed to easily tune the size of polypeptide-based, thermoresponsive hydrogel particles, from the nano- to microscale, using a single starting material. Particle size is controlled by the self-assembly and unique phase transition behavior of elastin-like polypeptides in bulk and within microfluidic-generated droplets. These particles are then stabilized through ultraviolet irradiation of a photo-crosslinkable unnatural amino acid (UAA) cotranslationally incorporated into the parent polypeptide. The thermoresponsive property of these particles provides an active mechanism for actuation and a dynamic responsive to the environment. This work represents a fundamental advance in the generation of crosslinked biomaterials, especially in the form of soft matter colloids, and is one of the first demonstrations of successful use of UAAs in generating a novel material.
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Affiliation(s)
- Simone A Costa
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Joseph R Simon
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University, P.O 653, Beer-Sheva, 8410501, Israel
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Lei Tang
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, USA
| | - Stefan Zauscher
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, USA
| | - Eric M Brustad
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Ashutosh Chilkoti
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
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Abstract
The genetic code-the language used by cells to translate their genomes into proteins that perform many cellular functions-is highly conserved throughout natural life. Rewriting the genetic code could lead to new biological functions such as expanding protein chemistries with noncanonical amino acids (ncAAs) and genetically isolating synthetic organisms from natural organisms and viruses. It has long been possible to transiently produce proteins bearing ncAAs, but stabilizing an expanded genetic code for sustained function in vivo requires an integrated approach: creating recoded genomes and introducing new translation machinery that function together without compromising viability or clashing with endogenous pathways. In this review, we discuss design considerations and technologies for expanding the genetic code. The knowledge obtained by rewriting the genetic code will deepen our understanding of how genomes are designed and how the canonical genetic code evolved.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511;
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; .,Department of Chemistry, Yale University, New Haven, Connecticut 06511
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45
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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